Metabolomics Python Packages

pyopenms

The codebase of the OpenMS project

249K 603 430

matchms

Python library for processing (tandem) mass spectrometry data and for computing spectral similarities.

50K 259 80

nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

9K 48 12

metbit

Metbit is an python package to analyse metabolomics

9K 3 0

depthcharge-ms

A deep learning toolkit for mass spectrometry

4K 95 27

pyopls

A Python 3 implementation of orthogonal projection to latent structures

3K 65 20

msbuddy

a python package for molecular formula analysis in MS-based small molecule studies

2K 37 8

isocor

IsoCor: Isotope Correction for mass spectrometry labeling experiments

2K 25 9

pygoslin

Python implementation of parsers for the Grammars on succinct lipid nomenclature (Goslin).

2K 4 2

find-mfs

A Python package for finding molecular formulae candidates which fit some given mass (+/- an error window). Uses Böcker & Lipták's highly efficient algorithm, as implemented in SIRIUS. This package also implements methods for filtering MF candidates by chemical rules, and simulated isotope envelopes.

2K 5 1

corems

Mass Spectrometry Framework for Small Molecules Analysis

1K 66 39

pymultiomics

Python toolbox for multi-omics data mapping and analysis

1K 28 6

metaspace2020

Cloud engine and platform for metabolite annotation for imaging mass spectrometry

1K 58 14

mbpls

(Multiblock) Partial Least Squares Regression for Python

1K 33 8

msi-recal

Cloud engine and platform for metabolite annotation for imaging mass spectrometry

1K 58 14

pi-metaboqc

A comprehensive LC-MS metabolomics quality-control and preprocessing package that provides an object-oriented pipeline for dataset construction, sample and feature filtering, signal drift and batch-effect correction, missing-value imputation, normalization, quality assessment, and report generation.

1K 2 0

pi-oplsda

A high-performance, pythonic implementation of Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA), tailored for metabolomics and bioinformatics

991 1 0

ms-mint

Python library for large-scale targeted metabolomics.

793 23 4

biosynfoni

a *biosynformatic* fingerprint to explore natural product distance and diversity

774 24 4

ms-mint-app

Web-based post-processing tool for LC-MS metabolomics data. Extract, visualize, and analyze targeted metabolites with interactive browser-based interface.

765 6 2